ElDorado / Gene2Promoter Release Notes
- ElDorado Data
- 15 updated genomes and new transcript annotation for all 33 organisms
- updated dbSNP (build 137) and mirBase (release 19) data
- new matrix library for transcription factors (1381 matrices in 411 families) and
model library
- ElDorado
- Transcriptome Viewer
- Expression values from BAM files can directly be visualized:
- BAM files that have been uploaded to the project management can be selected
in the analyses list
- expression analysis is done on the fly
- exons are colored according to their expression value
- comparative Bisulphite-Seq analysis (differential promoter methylation)
- Genome Browser
- reads are colored according to strand
- improved display of annotations in list view
- visualization of PFAM domains
- visualization of mapping quality (BAM files)
- keyword search allows transcript accession numbers
- transcripts can be highlighted by source (e.g. RefSeq or Ensembl only)
- visualization of paired-end reads
- connecting mates pairs
- highlighting inter-chromosomal read pairs
- highlighting read pairs deviating from expected insert size
- Genome Browser
- Visualization of BAM files: alignment view and coverage view
- Display of position on genome with cytobands, including stain information
- Display of Genomatix curated data tracks, currently available
- chromatin states of various cell types, according to Jason Ernst et al., Nature 473: 43-49 (2011)
- constrained elements: genomic elements under evolutionary constraint (identified by comparative analysis of 29 mammalian genomes) according to Lindblad-Toh et al., Nature 478: 476-482 (2011)
- Saving and loading of current state
- History: go back or forward to undo or redo the latest steps
- Easy extraction of selected sequences
- ElDorado Data
-
The ElDorado database now additionally contains microRNA hairpin structures that have been transmapped to all species available in ElDorado
- Transcriptome Viewer
- Improved paired end chart
- Distance points are split into upstream and downsteam distance points
- Visualization for bisulfite analysis
- Methylation data is used for promoter coloring
- Included Gene Fusion information
- breakpoint visualization
- coverage profile
- amino acid sequence of fused transcript
ElDorado: Detailed Transcript Information
- protein sequence in "exon-corresponding stretches"
- changed colouring scheme
- exon numbers as mouse-over
- New genomes:
- Oryctolagus cuniculus (rabbit, NCBI build 1)
- Xenopus tropicalis (western clawed frog, NCBI build 1)
- Updated genomes:
- Arabidopsis thaliana (TAIR 10)
- Bos taurus (NCBI build 5)
- Danio rerio (NCBI build 4)
- Sus scrofa (NCBI build 2)
- Discontinued ElDorado versions:
- ElDorado 07-2008
- ElDorado 12-2008
- Completely new Genome Browser
- Flash-based Genome Browser
- User-friendly browsing of genomes and all annotations as available in the ElDorado database
- Allows accessing a genome via position or going directly to a gene of interest
- Intuitive view of locus complexity
- Direct visualization of BED files (no need for preselecting "user data" in ElDorado)
- Various display formats and export options
- Transcriptome Viewer for alternative transcripts
- Detection of new splice junctions by integrating splice junction mappings
- New feature: Transcriptome Viewer for alternative transcripts
- Integration of exons, expression values, splice junctions and promoters in one view
- Integration of RNASeq data from GMS
- Classic view: each transcript is drawn separately
- Splicing graph view: identical exons are merged to depict a splicing graph
- Transcripts can be highlighted or filtered
- Several export options
- Available from navigation bar, "More Gene Info" and "Alternative Transcripts" in ElDorado
- New genomes:
- Soybean / Glycine max (Glyma 1)
- Corn / Zea mays (B73 RefGen v2)
- Carpenter ant / Camponotus floridanus (UPenn v3.3)
- Jumping ant / Harpegnathos saltator (UPenn v3.3)
- Neurospora crassa (Broad NC10)
- Plasmodium falciparum (NCBI build 1)
- Updated genome:
- Arabidopsis thaliana (TAIR 9)
- Homology groups including up to five orthologous insect genes are defined.
- Literature Analysis now links to the Genomatix Pathway System
(GePS)
- New Genomatix look & feel
- Improved handling of large User-specific data sets
New features and main changes from Release 4.8:
- New genomes:
- Wine grape / Vitis vinifera (NCBI build 1)
- Western balsam poplar / Populus trichocarpa (NCBI build 1)
- Sorghum / Sorghum bicolor (NCBI build 0.1)
- Zebra finch / Taeniopygia guttata (NCBI build 1)
- Updated genome:
- Homo sapiens (NCBI build 37 / hg19)
- Homology groups including up to five orthologous plant genes are defined.
New features and main changes from Release 4.7:
- New genomes:
- Saccharomyces cerevisiae (NCBI build 2)
- Schizosaccharomyces pombe (NCBI build 1)
- Updated genome:
- Oryza sativa (TIGR release 6)
- Inclusion of mitochondrial chromosomes for all genomes.
- Genomic regions can be selected by entering the chromosome (e.g. chr1) as alternative to the accession number of the contig.
- "Gene2Promoter - large scale": input of cDNA accession numbers is supported in order to allow retrieval of transcript specific promoters.
New features and main changes from Release 4.6:
- New genome:
- Sus scrofa (NCBI build 1: chromosomes 1, 4, 5, 7, 11, 13, 14, 15, 17,
and X)
- Updated genomes:
- Bos taurus (NCBI build 4)
- Danio rerio (NCBI build 3)
- Equus caballus (NCBI build 2)
- "Detailed Graphics": density plot of uploaded user data sets (e.g. reads from NGS analysis) added.
New features and main changes from Release 4.5.1:
- Transcripts from Ensembl Release 49 are now integrated into Eldorado as an additional data source.
- Only transcripts having a exon/intron structure different from the transcripts so far annotated in Eldorado are fully accessible.
- Transcripts with redundant exon/intron structure are only listed on the "More Gene Info" page.
- All transcripts can be searched by symbol and gene name
and additionally by their Ensembl gene and transcript IDs (e.g. ENSG00000009724, ENST00000376967).
New features and main changes from Release 4.5:
- TF binding site analysis of a promoter displays a tabular
output in addition to the graphical output.
New features and main changes from Release 4.4:
- New genomes:
- Equus caballus (NCBI build 1)
- Ornithorhynchus anatinus (NCBI build 1)
- Updated genomes:
- Mus musculus (NCBI build 37)
- New elements: inter-species highly conserved regions
- Many "CompGen promoters" have been annotated with
cross-mapped transcripts from other organisms (transcripts of these
promoters are marked with the species in the Gene2Promoter and
Comparative Genomics output.
- "General Gene Info" now also lists homology groups
for a gene and associated pathways (from
LitInspector)
- GPD is integrated into Gene2Promoter, i.e. all licensed
GenomatixSuite customers have the possibility to download large sets
of promoter sequences (called "Gene2Promoter - large scale"").
- The number of sequences to analyze with the regular
Gene2Promoter version (including interactive analysis) is increased from
50 to 1000.
- Promoters of "less relevant" transcripts are marked and can be
de-selected so that they do not influence the
FrameWorker analysis.
New features and main changes from Release 4.3:
- New genome:
- Monodelphis domestica (NCBI build 2)
- Updated genomes:
- Anopheles gambiae (NCBI build 2 v2)
- Apis mellifera (NCBI build 4)
- Bos taurus (NCBI build 3)
- Caenorhabditis elegans (NCBI WS160)
- Danio rerio (NCBI build 2)
- Drosophila melanogaster (NCBI build 5)
- Gallus gallus (NCBI build 2)
- Macaca mulatta (NCBI build 1)
- Oryza sativa (TIGR release 5)
- Pan troglodytes (NCBI build 2)
- Rattus norvegicus (NCBI build 4)
- The interactive SVG graphics is replaced by Genomatix
Java Graphics.
- The interactive graphics is implemented as Java applet, running within
your web browser requiring a Java plug-in.
- The Genomatix Java Graphics is faster than the SVG graphics and has more
features (e.g. exporting selected regions of the graphics). For more
details see the
graphics overview.
- User-defined data sets (data sets to be displayed only for
certain users) can be defined in the ElDorado database. To upload your data into ElDorado,
please contact us at support@genomatix.de
- Improved mapping algorithm for short sequences (< 500
base pairs).
- Transcription start sites (TSS) and clusters of CAGE tags
are combined to Transcription Start Regions (TSR). For each TSR (human and
mouse), detailed information on the tissue distribution of the CAGE tags is
available ("Tissue Profiles").
- CAGE tags are used as additional criteria to assign gold
quality to transcripts. A transcript gets gold quality if at least 3 CAGE
tags are located in the region ± 3 base pairs around the start of
the transcript.
- dbSNP IDs (e.g. rs11557697) and microRNA IDs from miRBase
(e.g. mmu-mir-668 or MI0004134) can be searched as keywords. In case the
element corresponding to the keyword is not located close to a known
gene, the genomic context (without gene information) is displayed in
ElDorado.
- "Annotation & Analysis": elements annotated
on the (+) strand and elements annotated on the (-) strand are displayed in
two separate tables.
- Gene2Promoter: In case the input is a transcript specific
identifier (e.g. Affymetrix ID, cDNA accession number, Genomatix transcript
ID), promoters of these transcripts are pre-selected in the output, all other
promoters of the corresponding gene are listed for the sake of completeness.
New features and main changes from Release 4.2:
- New Project Management:
- "Result Management" and "Sequence Management"
have been combined into the new "Project Management".
- Grouping of results and sequences into projects possible.
- Comments can be added to projects and results.
- Additional annotations:
- Transcription start sites defined by Riken CAGE tags (human, mouse)
- microRNA sequences (from the miRBase of the Sanger Institute)
- Detailed transcript information including
- information on the transcript like transcript quality, genomic location,
mapping quality, ...
- tissue information derived from CAGE tags and ESTs
- cDNA sequence and protein sequence
- Gene2Promoter output includes additional support for promoter
sequences:
- conservation in orthologous loci
- number of available CAGE tags
New features and main changes from Release 4.1:
- New genomes:
- Macaca mulatta (NCBI pre-release)
- Updated genomes:
- Homo sapiens (NCBI build 36)
- Mus musculus (NCBI build 36)
- Oryza sativa (TIGR release 4)
- Gene2Promoter: Selection of promoter sequences containing
certain transcription factor binding sites possible.
New features and main changes from Release 4.0:
- New genomes:
- Apis mellifera (NCBI build 2)
- Caenorhabditis elegans (NCBI)
- Danio rerio (NCBI build 1)
- Updated genomes:
- Bos taurus (NCBI build 2)
- Canis familiaris (NCBI build 2)
- Mus musculus (NCBI build 35)
- Enhanced definition of homology groups by exhaustive cross-mapping
of all transcripts between the different organisms.
- 25,116 vertebrate homology groups defined.
- 3005 homology groups contain all vertebrates in ElDorado (human, chimpanzee,
rat, mouse, zebrafish, chicken, dog, cow).
- Homology groups do not contain paralogs.
- New ultra fast algorithm for mapping sequences onto genomes.
- Completely revised display of literature information.
- "Gene <-> Gene Co-citations" and "Gene
<-> Transcription Factor Co-citations" have been merged to "Literature
Analysis".
- All Co-citation filter levels (like Abstract, Sentence) are displayed
in the same table.
- Direct links to BiblioSphere are provided for each co-cited gene.
- "More Gene Info" provides links to external database
like EntrezGene or Ensembl.
- Switch between different ElDorado databases possible.
- The ElDorado database version used is displayed at the top of each
ElDorado result.
- Default is the current ElDorado database "ElDorado 04-2006 (April
2006)". It can be changed to the previous version
"ElDorado 12-2005 (December 2005)" via the
"Personal" page of your account.
New features and main changes from Release 3.4.1:
- New genome:
- Bos taurus (NCBI build 1)
- Updated genomes:
- Canis familiaris (NCBI build 1)
- Oryza sativa (TIGR release 3)
- Pan troglodytes (NCBI build 1)
- Rattus norvegicus (NCBI build 3)
- Completely revised genome annotation:
- The genome annotation is performed by mapping of mRNA/cDNA sequences
to the NCBI genomes (using the Genomatix proprietary mapping algorithms).
- The quality of the annotation is heavily improved because incomplete
mapping of mRNAs does occur very rarely with the Genomatix mapping algorithms.
- Genomatix identifiers are assigned to
- loci (GXL_)
- transcripts (GXT_)
- promoters (GXP_)
- Enhanced definition of homology groups of orthologous genes:
- The transcripts annotated in ElDorado are aligned against each other
exhaustively. The pairwise sequence similarity is used to build homology
groups covering up to seven vertebrate genomes.
- The data from HomoloGene (NCBI) is evaluated for consistency and used
to complete the homology groups.
- Assignment of Affymetrix probe set identifiers to transcripts:
- The assignment of Affymetrix probe set identifiers to transcripts is
based on genomic mapping of each single probe. Chip probes from fifteen
human, mouse, and rat Affymetrix chips are available.
- The mapped single probes are displayed in the "Detailed Graphics",
the
"Annotation & Analysis", and the "Transcripts
& Probe Sets" output of ElDorado.
- When Affymetrix identifiers are used as input, a transcript will be
displayed if at least one single oligo-nucleotide probe of the probe
set (usually 11 probes) matches. For mixed probe sets (cross-hybridisation)
all relevant transcripts are displayed.
- Loci to be displayed in the "Comparative Genomics" output
of ElDorado can be selected/deselected by the user.
- "More Gene Info" additionally displays manually
curated information on interactions of transcription factors with genes including
the corresponding PubMed reference. (e.g. STAT6 regulates IL4R. The interaction
is activating, direct, and transcriptional. The information is derived from
PubMed ID 8810328.)
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